title: The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads.
abstract: BACKGROUND
  Next generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational approaches to evaluate the repetitive component of the genome of sunflower, by using medium/low coverage Illumina or 454 libraries.
  
  
  RESULTS
  By varying sequencing technology (Illumina or 454), coverage (0.55 x-1.25 x), assemblers and assembly procedures, six different genomic databases were produced. The annotation of these databases showed that they were composed of different proportions of repetitive DNA families. The final assembly of the sequences belonging to the six databases produced a whole genome set of 283,800 contigs. The redundancy of each contig was estimated by mapping the whole genome set with a large Illumina read set and measuring the number of matched Illumina reads. The repetitive component amounted to 81% of the sunflower genome, that is composed mainly of numerous families of Gypsy and Copia retrotransposons. Also many families of non autonomous retrotransposons and DNA transposons (especially of the Helitron superfamily) were identified.
  
  
  CONCLUSIONS
  The results substantially matched those previously obtained by using a Sanger-sequenced shotgun library and a standard 454 whole-genome-shotgun approach, indicating the reliability of the proposed procedures also for other species. The repetitive sequences were collected to produce a database, SUNREP, that will be useful for the annotation of the sunflower genome sequence and for studying the genome evolution in dicotyledons.
authors.affiliation: Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy. lnatali@agr.unipi.it.
authors.forename: Lucia
authors.initials: L
authors.lastname: Natali
authors.forename: Rosa Maria
authors.initials: RM
authors.lastname: Cossu
authors.forename: Elena
authors.initials: E
authors.lastname: Barghini
authors.forename: Tommaso
authors.initials: T
authors.lastname: Giordani
authors.forename: Matteo
authors.initials: M
authors.lastname: Buti
authors.forename: Flavia
authors.initials: F
authors.lastname: Mascagni
authors.forename: Michele
authors.initials: M
authors.lastname: Morgante
authors.forename: Navdeep
authors.initials: N
authors.lastname: Gill
authors.forename: Nolan C
authors.initials: NC
authors.lastname: Kane
authors.forename: Loren
authors.initials: L
authors.lastname: Rieseberg
authors.forename: Andrea
authors.initials: A
authors.lastname: Cavallini
mesh_terms: D001483:Base Sequence; D021901:DNA, Intergenic / Q000235:genetics; D030561:Databases, Nucleic Acid; D017343:Genes, Plant; D018745:Genome, Plant / Q000235:genetics*; D006368:Helianthus / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D018626:Retroelements / Q000235:genetics; D020079:Terminal Repeat Sequences / Q000235:genetics
chemical_list: D021901:DNA, Intergenic; D018626:Retroelements